A heading here

Posted by John Doe

Modify report_header.html for customization

1 About The Test: Variant Detection from RNA-seq

snpReportR: A Method for RNAseq Variant Detection Reporting

snpReportR: A Method for RNAseq Variant Detection Reporting

Patient details:
Information Value
Name: Jane Doe
DOB: 01/01/1900
Sex: F
Sample Type: RNA
Test ordered by:
Information Value
Name: Dr.X
Doctor identification number: 12345
Hospital: NCI

This document will help you to understand the more important findings from a gene variant screening. The common definitions of the type of genetic variants (mutations) are described in the figure and in the table in section Chromosome and Gene Vizualization of Mutations.

While a variant may have been detected, the associations with the variant are not perfectly causal and their complex interactions between biology and the environment.


2 About the Dataset

Table 1. Column names and Descriptions

In addition there are functional annotations for the variants per transcript from snpEFF. These include:

  • “Annotation_Impact”
  • “Feature_Type”
  • “Transcript_BioType”
  • “Rank”
  • “HGVS.c”
  • “HGVS.p”
  • “cDNA.pos/cDNA.length”
  • “CDS.pos/CDS.length”
  • “AA.pos/AA.length”
  • “Distance”

The top variants were ranked by the following attributes:

  • FATHMM predicted pathogenicty or splice adjacent
  • CHASMplus predicts driver mutations
  • genes with larger number of SNVs prioritized
  • high or moderate impact on the structure of the gene
  • CADD Score/Polyphen Score (not done yet)

Interpretation of attributes





3 HumanMine Annotation for Further Results

## [1] "COPA"    "PYCRL"   "FCHSD2"  "FSCN1"   "DCUN1D5"

Expression of Genes with identified variants/SNVs in Normal Tissues.


4 Results Table

Included here are two tables for different gene types. Coding refers to genes that produce proteins, while non-coding refers to genes which do get utilized to produce proteins.

4.1 Coding Genes

4.2 Non-Coding Genes


5 Chromosome and Gene Vizualization of Mutations

Table 6. Types of Expressed Variants
Type Description
coding: Mutation is within a coding region
5prime_UTR: Mutation is within 5’ untranslated region
3prime_UTR: Mutation is with 3’ untranslated region
introninc: Mutation is with an intron region
splice: Mutation is within proximity to a splice-site.
synonymous_variant: Synonymous variant is a mutation in an exon that results in same amino acid (changed codon)
missense_variant: Missense variant is a mutation in an exon that results in a different amino acid (changed codon)
start/stop: Mutation is within a start/stop codon.

Figure 1. Percentage of different types of mutations identified.

Figure 1. Percentage of different types of mutations identified.



# Add Lollipop plot - interactive

6 Expression of Genes with Mutations

6.1 boxplots/violin plots

Symbol GeneID DRR132310_H1299_1.0.bam DRR132321_H1299_0.1.bam DRR132333_H1299_.01.bam DRR131576_A549_1.0.bam DRR131588_A549_0.1.bam DRR131599_A549_.01.bam
COPA 1314 7.24 7.21 7.15 7.39 8.49 8.20
BCCIP 56647 7.14 7.51 6.59 6.91 6.72 7.24
FCHSD2 9873 5.17 4.72 5.20 5.38 3.39 4.54
DCUN1D5 84259 6.57 6.52 7.29 6.11 6.18 5.96
FSCN1 6624 4.79 3.44 4.59 4.79 5.00 5.56
MTM1 4534 4.87 4.80 3.68 4.47 4.75 4.94

Expression of the genes with pathogenic variants identified.

6.2 DE genes by condition

7 Sommelier results: Haplyotype/PCA

# add results here





8 What Does This Result Mean for you? And What’s Next?

Genetic tests sometimes reveal information that could be relevant to your family such as a health risk that might run in the family, or that family relationships are different from what you expected.

Can you please add this message in the next steps section, if the report show an association with a gene. Please contact your doctor and a genetic counselor. A genetic counselor can help you understand:




  1. how your family members may be affected if the test shows a serious health condition runs in your family.
  2. the risk of you and your partner passing on a health condition to your children your options if you have a child with an inherited health condition and you do not want your next child to inherit it
  3. genetic counselor can also direct you to relevant patient support group
# Need diagram here








9 More information

9.1 Recent Publications




9.2 Potential Drug Targets

Can search for additional drugs that may target the mutant genes online using Drug Targetor and at Drug Gene Interaction Database

# add drug target data information

9.3 Potential Clinical Trials

# search API at https://clinicaltrials.gov/api/

9.4 Web resources

# Add QR code where does it go?








11 Quality Control

11.1 Embed the IGV output from CTAT Mutation pipeline.

# embed file here

11.2 Sequencing Depth and QC

# include Deeptools plots for coverage, average
# base quality scores, alignment quality scores,
# etc.








12 References:

12.1 Citations

Smith RN, et al. InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data. Bioinformatics. 2012 Dec 1;28(23):3163-5.

12.2 Genome References and Software

12.3 Additional information about the pipelines used, check out the github repositories listed below:







## TxDb object:
## # Db type: TxDb
## # Supporting package: GenomicFeatures
## # Data source: ~/Downloads/gencode.v22.annotation.gtf.gz
## # Organism: NA
## # Taxonomy ID: NA
## # miRBase build ID: NA
## # Genome: NA
## # Nb of transcripts: 198442
## # Db created by: GenomicFeatures package from Bioconductor
## # Creation time: 2021-03-30 19:49:41 -0700 (Tue, 30 Mar 2021)
## # GenomicFeatures version at creation time: 1.42.2
## # RSQLite version at creation time: 2.2.5
## # DBSCHEMAVERSION: 1.2




12.4 Session Information

sessionInfo()
## R version 4.0.4 (2021-02-15)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Catalina 10.15.7
## 
## Matrix products: default
## BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
##  [1] grid      stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] Gviz_1.34.1                 InterMineR_1.12.0           VariantAnnotation_1.36.0    Rsamtools_2.6.0            
##  [5] Biostrings_2.58.0           XVector_0.30.0              SummarizedExperiment_1.20.0 MatrixGenerics_1.2.1       
##  [9] matrixStats_0.58.0          vcfR_1.12.0                 RColorBrewer_1.1-2          gridExtra_2.3              
## [13] ggplot2_3.3.3               shiny_1.6.0                 stringr_1.4.0               magrittr_2.0.1             
## [17] knitr_1.31                  GenomicFeatures_1.42.2      AnnotationDbi_1.52.0        Biobase_2.50.0             
## [21] GenomicRanges_1.42.0        GenomeInfoDb_1.26.4         IRanges_2.24.1              S4Vectors_0.28.1           
## [25] BiocGenerics_0.36.0         here_1.0.1                  rmarkdown_2.7               tidyr_1.1.3                
## [29] dplyr_1.0.5                 snpReportR_0.0.0.9          devtools_2.3.2              usethis_2.0.1              
## 
## loaded via a namespace (and not attached):
##   [1] utf8_1.2.1               proto_1.0.0              tidyselect_1.1.0         RSQLite_2.2.5            htmlwidgets_1.5.3       
##   [6] BiocParallel_1.24.1      munsell_0.5.0            chron_2.3-56             DT_0.17                  withr_2.4.1             
##  [11] colorspace_2.0-0         highr_0.8                rstudioapi_0.13          labeling_0.4.2           GenomeInfoDbData_1.2.4  
##  [16] bit64_4.0.5              farver_2.1.0             rprojroot_2.0.2          vctrs_0.3.6              generics_0.1.0          
##  [21] xfun_0.22                biovizBase_1.38.0        BiocFileCache_1.14.0     R6_2.5.0                 RJSONIO_1.3-1.4         
##  [26] AnnotationFilter_1.14.0  bitops_1.0-6             cachem_1.0.4             DelayedArray_0.16.3      assertthat_0.2.1        
##  [31] promises_1.2.0.1         scales_1.1.1             pinfsc50_1.2.0           nnet_7.3-15              debugme_1.1.0           
##  [36] gtable_0.3.0             processx_3.5.0           ensembldb_2.14.0         rlang_0.4.10             systemfonts_1.0.1       
##  [41] splines_4.0.4            rtracklayer_1.50.0       lazyeval_0.2.2           gargle_1.0.0             dichromat_2.0-0         
##  [46] checkmate_2.0.0          yaml_2.2.1               tidytext_0.3.0           backports_1.2.1          crosstalk_1.1.1         
##  [51] httpuv_1.5.5             tokenizers_0.2.1         Hmisc_4.5-0              tools_4.0.4              ellipsis_0.3.1          
##  [56] kableExtra_1.3.4         jquerylib_0.1.3          sessioninfo_1.1.1        gsubfn_0.7               Rcpp_1.0.6              
##  [61] base64enc_0.1-3          progress_1.2.2           zlibbioc_1.36.0          purrr_0.3.4              RCurl_1.98-1.3          
##  [66] ps_1.6.0                 prettyunits_1.1.1        rpart_4.1-15             openssl_1.4.3            sqldf_0.4-11            
##  [71] cluster_2.1.1            fs_1.5.0                 data.table_1.14.0        SnowballC_0.7.0          ProtGenerics_1.22.0     
##  [76] pkgload_1.2.0            hms_1.0.0                mime_0.10                evaluate_0.14            xtable_1.8-4            
##  [81] XML_3.99-0.6             jpeg_0.1-8.1             gmailr_1.0.0             testthat_3.0.2           compiler_4.0.4          
##  [86] biomaRt_2.46.3           tibble_3.1.0             crayon_1.4.1             htmltools_0.5.1.1        mgcv_1.8-34             
##  [91] later_1.1.0.1            Formula_1.2-4            DBI_1.1.1                formatR_1.8              dbplyr_2.1.0            
##  [96] MASS_7.3-53.1            rappdirs_0.3.3           Matrix_1.3-2             permute_0.9-5            cli_2.3.1               
## [101] igraph_1.2.6             pkgconfig_2.0.3          GenomicAlignments_1.26.0 foreign_0.8-81           plotly_4.9.3            
## [106] xml2_1.3.2               svglite_2.0.0            bslib_0.2.4              webshot_0.5.2            rvest_1.0.0             
## [111] janeaustenr_0.1.5        callr_3.6.0              digest_0.6.27            vegan_2.5-7              htmlTable_2.1.0         
## [116] curl_4.3                 lifecycle_1.0.0          nlme_3.1-152             jsonlite_1.7.2           desc_1.3.0              
## [121] viridisLite_0.3.0        askpass_1.1              BSgenome_1.58.0          fansi_0.4.2              pillar_1.5.1            
## [126] lattice_0.20-41          fastmap_1.1.0            httr_1.4.2               pkgbuild_1.2.0           survival_3.2-10         
## [131] glue_1.4.2               remotes_2.2.0            png_0.1-7                blastula_0.3.2           bit_4.0.4               
## [136] stringi_1.5.3            sass_0.3.1               blob_1.2.1               latticeExtra_0.6-29      memoise_2.0.0           
## [141] ape_5.4-1